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Bioinformatics. 2016 Feb 1;32(3):354-61. doi: 10.1093/bioinformatics/btv584. Epub 2015 Oct 9.

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.

Author information

1
Computational Science Research Center.
2
Department of Biology, San Diego State University, San Diego, CA 92182, USA.
3
Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, The Netherlands Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Brazil.
4
Computational Science Research Center Department of Biology, San Diego State University, San Diego, CA 92182, USA Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Brazil Department of Computer Science, San Diego State University, San Diego, CA 92182, USA Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, IL 60439, USA.

Abstract

SUMMARY:

Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.

AVAILABILITY AND IMPLEMENTATION:

SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS.

CONTACT:

redwards@mail.sdsu.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26454280
PMCID:
PMC4734042
DOI:
10.1093/bioinformatics/btv584
[Indexed for MEDLINE]
Free PMC Article

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